Structure and genetic diversity of macauba [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] approached by SNP markers to assist breeding strategies

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

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Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers

Plant Genetic Resources ◽

10.1017/s1479262121000034 ◽

2021 ◽

Vol 19 (1) ◽

pp. 20-28

Author(s):

Abush Tesfaye Abebe ◽

Adesike Oladoyin Kolawole ◽

Nnanna Unachukwu ◽

Godfree Chigeza ◽

Hailu Tefera ◽

...

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Glycine Max ◽

Snp Markers ◽

Fixation Index ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Breeding Lines ◽

Soybean Germplasm ◽

Elite Breeding Lines

AbstractSoybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

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All Populations Matter: Conservation Genomics of Australia’s Iconic Purple Wattle, Acacia purpureopetala

Diversity ◽

10.3390/d13040139 ◽

2021 ◽

Vol 13 (4) ◽

pp. 139

Author(s):

Marlien M. van der Merwe ◽

Jia-Yee S. Yap ◽

Peter D. Wilson ◽

Helen T. Murphy ◽

Andrew Ford

Keyword(s):

Genetic Diversity ◽

Allelic Variation ◽

Germplasm Conservation ◽

Snp Markers ◽

Genomic Diversity ◽

Ex Situ ◽

Spatial Distance ◽

Genetic Connectivity ◽

Conservation Genomics ◽

Modelling Framework

Maximising genetic diversity in conservation efforts can help to increase the chances of survival of a species amidst the turbulence of the anthropogenic age. Here, we define the distribution and extent of genomic diversity across the range of the iconic but threatened Acacia purpureopetala, a beautiful sprawling shrub with mauve flowers, restricted to a few disjunct populations in far north Queensland, Australia. Seed production is poor and germination sporadic, but the species occurs in abundance at some field sites. While several thousands of SNP markers were recovered, comparable to other Acacia species, very low levels of heterozygosity and allelic variation suggested inbreeding. Limited dispersal most likely contributed towards the high levels of divergence amongst field sites and, using a generalised dissimilarity modelling framework amongst environmental, spatial and floristic data, spatial distance was found to be the strongest factor explaining the current distribution of genetic diversity. We illustrate how population genomic data can be utilised to design a collecting strategy for a germplasm conservation collection that optimises genetic diversity. For this species, inclusion of all field sites will capture maximum genetic diversity for both in situ and ex situ conservation. Assisted cross pollination, within and between field sites and genetically structured groups, is recommended to enhance heterozygosity particularly at the most disjunct sites and further fragmentation should be discouraged to avoid loss of genetic connectivity.

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Genetic diversity evaluations in Turkish onion (Allium cepaL.) genotypes: principal component analyses (PCA) for breeding strategies

Acta Horticulturae ◽

10.17660/actahortic.2016.1143.33 ◽

2016 ◽

pp. 227-234

Author(s):

F. Hanci ◽

A.F. Gokce

Keyword(s):

Genetic Diversity ◽

Principal Component ◽

Breeding Strategies ◽

Principal Component Analyses

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Genetic Diversity and Differentiation of Northern Populations of Pedunculate Oak Based on Analysis of New SNP Markers

Russian Journal of Genetics ◽

10.1134/s1022795421030054 ◽

2021 ◽

Vol 57 (3) ◽

pp. 374-378

Author(s):

B. Degen ◽

Y. A. Yanbaev ◽

R. Y. Ianbaev ◽

S. Y. Bakhtina ◽

A. A. Gabitova ◽

...

Keyword(s):

Genetic Diversity ◽

Snp Markers ◽

Pedunculate Oak

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Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers

PeerJ ◽

10.7717/peerj.8038 ◽

2019 ◽

Vol 7 ◽

pp. e8038

Author(s):

Yanli Xiong ◽

Wenhui Liu ◽

Yi Xiong ◽

Qingqing Yu ◽

Xiao Ma ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Western China ◽

Tibet Plateau ◽

Group Method ◽

Breeding Strategies ◽

Population Genetic Differentiation ◽

Principal Coordinates ◽

Geographical Regions ◽

Genetic Diversity And Structure

Hosting unique and important plant germplasms, the Qinghai-Tibet Plateau (QTP), as the third pole of the world, and Xinjiang, located in the centre of the Eurasian continent, are major distribution areas of perennial Triticeae grasses, especially the widespread Elymus species. Elymus excelsus Turcz. ex Griseb, a perennial forage grass with strong tolerance to environmental stresses, such as drought, cold and soil impoverishment, can be appropriately used for grassland establishment due to its high seed production. To provide basic information for collection, breeding strategies and utilization of E. excelsus germplasm, microsatellite markers (SSR) were employed in the present study to determine the genetic variation and population structure of 25 wild accessions of E. excelsus from Xinjiang (XJC) and the QTP, including Sichuan (SCC) and Gansu (GSC) of western China. Based on the 159 polymorphic bands amplified by 35 primer pairs developed from three related species, the average values of the polymorphic information content (PIC), marker index (MI), resolving power (Rp), Nei’s genetic diversity (H) and Shannon’s diversity index (I) of each pair of primers were 0.289, 1.348, 1.897, 0.301 and 0.459, respectively, validating that these SSR markers can also be used for the evaluation of genetic diversity of E. excelsus germplasms, and demonstrating the superior versatility of EST-SSR vs. G-SSR. We found a relatively moderate differentiation (Fst = 0.151) among the XJC, SCC and GSC geo-groups, and it is worth noting that, the intra-group genetic diversity of the SCC group (He = 0.197) was greater than that of the GSC (He = 0.176) and XJC (He = 0.148) groups. Both the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) divided the 25 accessions into three groups, whereas the Bayesian STRUCTURE analysis suggested that E. excelsus accessions fell into four main clusters. Besides, this study suggested that geographical distance and environmental variables (annual mean precipitation and average precipitation in growing seasons), especially for QTP accessions, should be combined to explain the population genetic differentiation among the divergent geographical regions. These data provided comprehensive information about these valuable E. excelsus germplasm resources for the protection and collection of germplasms and for breeding strategies in areas of Xinjiang and QTP in western China.

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Genetic Diversity Analysis of 53 Indonesian Rice Genotypes using 6K Single Nucleotide Polymorphism Markers

Jurnal AgroBiogen ◽

10.21082/jbio.v14n1.2018.p1-10 ◽

2018 ◽

Vol 14 (1) ◽

pp. 1

Author(s):

Joko Prasetiyono ◽

Nurul Hidayatun ◽

Tasliah Tasliah

Keyword(s):

Genetic Diversity ◽

Morphological Characters ◽

Snp Markers ◽

Japonica Rice ◽

Rice Varieties ◽

Tropical Japonica ◽

Rice Chromosomes ◽

Improvement Programs ◽

Rice Genotypes ◽

Genotypic Mixtures

<p>Indonesia is rich in rice genetic resources, however, only a small number has been used in variety improvement programs. This study aimed to determine the genetic diversity of Indonesian rice varieties using 6K SNP markers. The study was conducted at ICABIOGRAD for DNA isolation and IRRI for SNP marker analysis. Genetic materials were 53 rice genotypes consisting of 49 varieties and 4 check genotypes. SNP markers used were 6K loci. Results showed that among the markers analyzed, only 4,606 SNPs (76.77%) were successfully read. The SNP markers covered all twelve rice chromosomes of 945,178.27 bp. The most common allele observed was GG, whereas the least allele was TG. Dendrograms of the 53 rice varieties analyzed with 4,606 SNPs demonstrated several small groups containing genotypic mixtures between indica and japonica rice, and no groups were found to contain firmly indica or japonica type. Structure analysis (K = 2) with value of 0.8 showed that the 53 rice varieties were divided into several groups and each group consisted of 4 japonica, 2 tropical japonica, 46 indica, and 1 aus rice type, respectively. IR64 and Ciherang proved to have an indica genome, while Rojolele has japonica one. Dupa and Hawara Bunar, usually grouped into tropical japonica rice, were classified as indica type, and Hawara Bunar has perfectly 100% indica type. The results of this study indicated that rice classification (indica-japonica) which is usually classified based only on morphological characters, e.g. grain and leaf shapes, is not enough and classification based on SNP markers should be considered for that purpose.</p>

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Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis ◽

10.11118/actaun201967061457 ◽

2019 ◽

Vol 67 (6) ◽

pp. 1457-1463 ◽

Cited By ~ 2

Author(s):

Radovan Kasarda ◽

Nina Moravčíková ◽

Ondrej Kadlečík ◽

Anna Trakovická ◽

Marko Halo ◽

...

Keyword(s):

Genetic Diversity ◽

Quality Control ◽

Genomic Analysis ◽

Genomic Data ◽

Reference Population ◽

Pedigree Analysis ◽

Snp Markers ◽

Runs Of Homozygosity ◽

Current Generation ◽

Genomic Inbreeding

The objective of this study was to analyse the level of pedigree and genomic inbreeding in a herd of the Norik of Muran horses. The pedigree file included 1374 animals (603 stallions and 771 mares), while the reference population consisted of animals that were genotyped by using 70k SNP platform (n = 25). The trend of pedigree inbreeding was expressed as the probability that an animal has two identical alleles by descent according to classical formulas. The trend of genomic inbreeding was derived from the distribution of runs of homozygosity (ROHs) with various length in the genome based on the assumption that these regions reflect the autozygosity originated from past generations of ancestors. A maximum of 19 generations was found in pedigree file. As expected, the highest level of pedigree completeness was found in first five generations. Subsequent quality control of genomic data resulted in totally 54432 SNP markers covering 2.242 Mb of the autosomal genome. The pedigree analysis showed that in current generation can be expected the pedigree inbreeding at level 0.23% (ΔFPEDi = 0.19 ± 1.17%). Comparable results was obtained also by the genomic analysis, when the inbreeding in current generation reached level 0.11%. Thus, in term of genetic diversity both analyses reflected sufficient level of variability across analysed population of Norik of Muran horses.

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